Modeling the binding affinity of peptides for graphitic surfaces. Influences of aromatic content and interfacial shape

Interactions between peptide sequences and graphitic surfaces-carbon nanotubes and graphite-are investigated using molecular dynamics simulations with a polarizable force-field. Peptide sequences selected to have a strong affinity for carbon nanotubes [Nat. Mater. 2003, 2, 196.] are rich in tryptophan. We investigate the importance of the tryptophan residue for two of these sequences by mutating each tryptophan with either tyrosine or phenylalanine. We find that, in line with recent experimental observations, the original, tryptophan-containing sequences support relatively stronger binding to both nanotubes and graphite, compared with the mutants. We ascribe this behavior to the additional structural stability conferred by the indole group at the interface. We also explore the effect of interfacial curvature on the binding affinity. Our findings suggest that these nanotube-binding peptides have also been selected for interfacial shape. For the graphite surface our results indicate a compromise exists between maintaining strong ring-surface interactions and allowing nonaromatic groups to also approach the surface